crystfel.git
3 hours agopeakFinder9: remove references to image.num_peaks etc master
Thomas White [Fri, 19 Jul 2019 14:17:25 +0000 (16:17 +0200)]
peakFinder9: remove references to image.num_peaks etc

8 hours agoIncrease maximum geometry length from stream
Thomas White [Fri, 19 Jul 2019 09:50:18 +0000 (11:50 +0200)]
Increase maximum geometry length from stream

It's already too small

2 days agozmq: Remove reference to image.num_peaks
Thomas White [Wed, 17 Jul 2019 12:55:13 +0000 (14:55 +0200)]
zmq: Remove reference to image.num_peaks

See 636eb6116961296791bae35c40fd9438aa946827

2 days agoMerge branch 'tom/zmq'
Thomas White [Wed, 17 Jul 2019 12:54:00 +0000 (14:54 +0200)]
Merge branch 'tom/zmq'

2 days agopartialator: Add "offset" model (Ewald sphere offset assuming monochromatic beam)
Thomas White [Wed, 17 Jul 2019 09:27:36 +0000 (11:27 +0200)]
partialator: Add "offset" model (Ewald sphere offset assuming monochromatic beam)

2 days agopartialator: Allow refinement of any partiality model
Thomas White [Wed, 17 Jul 2019 09:21:30 +0000 (11:21 +0200)]
partialator: Allow refinement of any partiality model

2 days agoDon't repeat scaling when refining
Thomas White [Fri, 5 Jul 2019 14:25:54 +0000 (16:25 +0200)]
Don't repeat scaling when refining

This seems to be a major cause of "going off the rails", and the
surfaces look reasonable (in fact, better) without it.  Plus, if the
user says --no-scale, there should be no scaling at all.

2 days agopartialator: Use Spectrum API
Thomas White [Thu, 27 Jun 2019 14:34:45 +0000 (16:34 +0200)]
partialator: Use Spectrum API

2 days agoComment out debug
Thomas White [Thu, 27 Jun 2019 12:04:16 +0000 (14:04 +0200)]
Comment out debug

2 days agoReally Simple Minimiser
Thomas White [Thu, 27 Jun 2019 12:04:06 +0000 (14:04 +0200)]
Really Simple Minimiser

2 days agoFix grid scan boundaries to put plot-pr-contourmap's red dot in the right place
Thomas White [Thu, 27 Jun 2019 11:23:44 +0000 (13:23 +0200)]
Fix grid scan boundaries to put plot-pr-contourmap's red dot in the right place

2 days agoImprove column headings in logs
Thomas White [Wed, 26 Jun 2019 14:58:33 +0000 (16:58 +0200)]
Improve column headings in logs

2 days agoDon't re-scale when calculating FoM during PR
Thomas White [Wed, 26 Jun 2019 14:56:55 +0000 (16:56 +0200)]
Don't re-scale when calculating FoM during PR

2 days agoModify residual some more
Thomas White [Tue, 25 Jun 2019 07:56:39 +0000 (09:56 +0200)]
Modify residual some more

2 days agoModify residual to give clearer minimum, particularly as function of profile radius
Thomas White [Thu, 20 Jun 2019 14:28:53 +0000 (16:28 +0200)]
Modify residual to give clearer minimum, particularly as function of profile radius

2 days agopartialator: WIP on new minimiser
Thomas White [Wed, 19 Jun 2019 08:55:56 +0000 (10:55 +0200)]
partialator: WIP on new minimiser

2 days agopartialator: Only strong reflections in specgraph, and remove resolution limit for...
Thomas White [Thu, 13 Jun 2019 09:19:25 +0000 (11:19 +0200)]
partialator: Only strong reflections in specgraph, and remove resolution limit for pgraph

Rationale for pgraph: the viewer already has a resolution selector.

2 days agopartial_sim: Use Spectrum API
Thomas White [Fri, 28 Jun 2019 11:39:35 +0000 (13:39 +0200)]
partial_sim: Use Spectrum API

2 days agoscripts/plot-pr: Allow the use of folder names other than "pr-logs"
Thomas White [Fri, 28 Jun 2019 09:36:11 +0000 (11:36 +0200)]
scripts/plot-pr: Allow the use of folder names other than "pr-logs"

2 days agoWeight reflections according to how much they need to be scaled up
Thomas White [Wed, 5 Jun 2019 09:32:21 +0000 (11:32 +0200)]
Weight reflections according to how much they need to be scaled up

2 days agoAllow correct_reflection() to correct anything, not just intensities
Thomas White [Wed, 5 Jun 2019 09:15:18 +0000 (11:15 +0200)]
Allow correct_reflection() to correct anything, not just intensities

3 days agoAdd matrix notation doc
Thomas White [Wed, 26 Jun 2019 14:58:52 +0000 (16:58 +0200)]
Add matrix notation doc

3 days agohdfsee: Disallow changing image if geometry file was given
Thomas White [Tue, 16 Jul 2019 15:10:06 +0000 (17:10 +0200)]
hdfsee: Disallow changing image if geometry file was given

3 days agohdfile_get_string_value(): Detect non-scalar string
Thomas White [Tue, 16 Jul 2019 15:09:05 +0000 (17:09 +0200)]
hdfile_get_string_value(): Detect non-scalar string

Handling strings in HDF5 is already a complete pain.  Eventually we
should handle an array of strings, but it's too hard for now.

3 days agohdfile_get_value(): Increase maximum number of dimensions to 64
Thomas White [Tue, 16 Jul 2019 15:08:25 +0000 (17:08 +0200)]
hdfile_get_value(): Increase maximum number of dimensions to 64

3 might be too low for a hypothetical file format with, say, two
wildcard dimensions.

3 days agoRemove warnings about non-scalar values
Thomas White [Tue, 16 Jul 2019 11:50:18 +0000 (13:50 +0200)]
Remove warnings about non-scalar values

Already handled by return codes.

3 days agoTidy up
Thomas White [Tue, 16 Jul 2019 11:37:05 +0000 (13:37 +0200)]
Tidy up

3 days agohdfsee: Get rid of "multi_event"
Thomas White [Tue, 16 Jul 2019 11:36:46 +0000 (13:36 +0200)]
hdfsee: Get rid of "multi_event"

3 days agohdfsee: Factorise setting of window title
Thomas White [Tue, 16 Jul 2019 11:33:52 +0000 (13:33 +0200)]
hdfsee: Factorise setting of window title

3 days agohdfsee: Get rid of "simple"
Thomas White [Tue, 16 Jul 2019 09:43:26 +0000 (11:43 +0200)]
hdfsee: Get rid of "simple"

3 days agohdfsee: Show HDF5 menu tree event for multi-event files
Thomas White [Tue, 16 Jul 2019 09:42:51 +0000 (11:42 +0200)]
hdfsee: Show HDF5 menu tree event for multi-event files

3 days agoGeneralise get_ev_based_value() to handle non-multievent case
Thomas White [Tue, 16 Jul 2019 09:33:05 +0000 (11:33 +0200)]
Generalise get_ev_based_value() to handle non-multievent case

... and replace hdfile_get_value() with it

2 weeks agoload_entire_file(): Ensure string termination
Thomas White [Fri, 5 Jul 2019 14:49:36 +0000 (16:49 +0200)]
load_entire_file(): Ensure string termination

2 weeks agoFormatting
Thomas White [Fri, 5 Jul 2019 10:06:11 +0000 (12:06 +0200)]
Formatting

2 weeks agoUpdate copyright dates
Thomas White [Fri, 5 Jul 2019 10:05:12 +0000 (12:05 +0200)]
Update copyright dates

2 weeks agogeoptimiser: Use geometry from stream, if present
Thomas White [Fri, 5 Jul 2019 10:04:29 +0000 (12:04 +0200)]
geoptimiser: Use geometry from stream, if present

Simply omit the -g option to use geometry from stream.

2 weeks agoAdd write_detector_geometry_3() (write geometry based on template in memory)
Thomas White [Fri, 5 Jul 2019 09:57:18 +0000 (11:57 +0200)]
Add write_detector_geometry_3() (write geometry based on template in memory)

2 weeks agoRead geometry file from start of stream
Thomas White [Fri, 5 Jul 2019 09:54:56 +0000 (11:54 +0200)]
Read geometry file from start of stream

2 weeks agoAdd get_detector_geometry_from_string()
Thomas White [Thu, 4 Jul 2019 12:31:43 +0000 (14:31 +0200)]
Add get_detector_geometry_from_string()

3 weeks agopartial_sim: Add --template-stream
Thomas White [Tue, 25 Jun 2019 15:11:09 +0000 (17:11 +0200)]
partial_sim: Add --template-stream

3 weeks agopartial_sim: Add missing initialisations
Thomas White [Tue, 25 Jun 2019 15:10:33 +0000 (17:10 +0200)]
partial_sim: Add missing initialisations

3 weeks agoread_stream_reflections_*: Set symmetric indices for reflections
Thomas White [Tue, 25 Jun 2019 15:09:51 +0000 (17:09 +0200)]
read_stream_reflections_*: Set symmetric indices for reflections

4 weeks agopartialator: Be more verbose about minimisation failures
Thomas White [Thu, 13 Jun 2019 09:20:21 +0000 (11:20 +0200)]
partialator: Be more verbose about minimisation failures

4 weeks agoFormatting
Thomas White [Wed, 5 Jun 2019 13:26:12 +0000 (15:26 +0200)]
Formatting

About the comment: yes, it is.  temp2 (T) has already been de-logged by
this point.

4 weeks agopartialator: Add --force-lambda
Thomas White [Thu, 20 Jun 2019 15:17:08 +0000 (17:17 +0200)]
partialator: Add --force-lambda

4 weeks agoActually prevent the use of free-flagged reflections in refinement
Thomas White [Thu, 20 Jun 2019 14:30:19 +0000 (16:30 +0200)]
Actually prevent the use of free-flagged reflections in refinement

Since we are now using residual() in a numerical minimisation, it's
important that it uses either only free-flagged reflections, or only
non-free-flagged ones.

4 weeks agoscripts/plot-pr-contourmap: Allow the use of folder names other than "pr-logs"
Thomas White [Thu, 20 Jun 2019 13:58:54 +0000 (15:58 +0200)]
scripts/plot-pr-contourmap: Allow the use of folder names other than "pr-logs"

4 weeks agopartialator: Progress bar for logs/grid scans
Thomas White [Wed, 19 Jun 2019 08:55:43 +0000 (10:55 +0200)]
partialator: Progress bar for logs/grid scans

4 weeks agopartialator: With --no-free, still show non-free residuals for crystals with too...
Thomas White [Wed, 12 Jun 2019 08:13:53 +0000 (10:13 +0200)]
partialator: With --no-free, still show non-free residuals for crystals with too few free reflections

4 weeks agoAdd missing newline
Thomas White [Fri, 14 Jun 2019 09:46:26 +0000 (11:46 +0200)]
Add missing newline

4 weeks agoRename scripts/plot-contourmap -> scripts/plot-pr-contourmap
Thomas White [Tue, 18 Jun 2019 11:39:53 +0000 (13:39 +0200)]
Rename scripts/plot-contourmap -> scripts/plot-pr-contourmap

4 weeks agoConst-cleanliness
Thomas White [Mon, 17 Jun 2019 09:17:33 +0000 (11:17 +0200)]
Const-cleanliness

4 weeks agopattern_sim: Fix uninitialised value
Thomas White [Tue, 18 Jun 2019 15:05:31 +0000 (17:05 +0200)]
pattern_sim: Fix uninitialised value

6 weeks agopartialator: Parallelise deltaCChalf calculation
Thomas White [Wed, 5 Jun 2019 14:49:45 +0000 (16:49 +0200)]
partialator: Parallelise deltaCChalf calculation

6 weeks agoFix obvious bug in image_add_feature()
Thomas White [Wed, 5 Jun 2019 13:46:40 +0000 (15:46 +0200)]
Fix obvious bug in image_add_feature()

Introduced by aa1676f35317df92840b27ba78f13c13308bc7d4

6 weeks agogpu_sim_check: Increase tolerance from 1.1% to 1.2%
Thomas White [Tue, 4 Jun 2019 15:11:11 +0000 (17:11 +0200)]
gpu_sim_check: Increase tolerance from 1.1% to 1.2%

1.13% deviation now observed in the wild, with no other problems.

6 weeks agospectrum_set_pdf: Use gsl_sort_index() instead of gsl_sort2()
Thomas White [Tue, 4 Jun 2019 15:05:50 +0000 (17:05 +0200)]
spectrum_set_pdf: Use gsl_sort_index() instead of gsl_sort2()

This allows compatibility with older versions of GSL.

6 weeks agocell_explorer: Avoid more GTK3-isms
Thomas White [Tue, 4 Jun 2019 14:28:28 +0000 (16:28 +0200)]
cell_explorer: Avoid more GTK3-isms

6 weeks agocell_explorer: Remove GTK3-isms
Thomas White [Tue, 4 Jun 2019 13:31:09 +0000 (15:31 +0200)]
cell_explorer: Remove GTK3-isms

7 weeks agoFix SASE simulation
Thomas White [Fri, 24 May 2019 17:47:50 +0000 (19:47 +0200)]
Fix SASE simulation

7 weeks agoSpectrum generation
Thomas White [Fri, 24 May 2019 15:08:04 +0000 (17:08 +0200)]
Spectrum generation

7 weeks agoNormalise sampled spectrum weights to total 1
Thomas White [Thu, 23 May 2019 14:42:27 +0000 (16:42 +0200)]
Normalise sampled spectrum weights to total 1

7 weeks agoRemove old debugging statement
Thomas White [Thu, 23 May 2019 14:42:16 +0000 (16:42 +0200)]
Remove old debugging statement

7 weeks agoUse Spectrum API for simulation
Thomas White [Fri, 17 May 2019 15:03:48 +0000 (17:03 +0200)]
Use Spectrum API for simulation

2 months agos/histogram/pdf/
Thomas White [Fri, 17 May 2019 15:03:28 +0000 (17:03 +0200)]
s/histogram/pdf/

2 months agoSpectrum API clarifications
Thomas White [Wed, 15 May 2019 15:02:21 +0000 (17:02 +0200)]
Spectrum API clarifications

2 months agoComplete implementation of Spectrum API
Thomas White [Wed, 15 May 2019 14:58:24 +0000 (16:58 +0200)]
Complete implementation of Spectrum API

2 months agoStart implementing Spectrum API
Thomas White [Tue, 14 May 2019 09:28:43 +0000 (11:28 +0200)]
Start implementing Spectrum API

2 months agoUpdate Spectrum API
Thomas White [Mon, 13 May 2019 13:09:58 +0000 (15:09 +0200)]
Update Spectrum API

2 months agoSketch out Spectrum API
Thomas White [Fri, 10 May 2019 11:59:38 +0000 (13:59 +0200)]
Sketch out Spectrum API

2 months agoUpdate coding standards
Thomas White [Thu, 9 May 2019 14:45:24 +0000 (16:45 +0200)]
Update coding standards

2 months agoRemove image.num_peaks and num_saturated_peaks
Thomas White [Wed, 8 May 2019 12:37:27 +0000 (14:37 +0200)]
Remove image.num_peaks and num_saturated_peaks

These values were inconsistently set by different parts of the code,
e.g. different peak search methods.  num_saturated_peaks was even set
during final integration.  Now, the peak count is taken from the
ImageFeatureList, so it's authoritative.

2 months agoMove Histogram out of API
Thomas White [Wed, 8 May 2019 11:54:18 +0000 (13:54 +0200)]
Move Histogram out of API

It's only used by two test programs

2 months agoAdd documentation for search_peaks_peakfinder8
Thomas White [Tue, 7 May 2019 15:32:05 +0000 (17:32 +0200)]
Add documentation for search_peaks_peakfinder8

2 months agoRemove old "statistics" module with R factors etc
Thomas White [Tue, 7 May 2019 15:25:50 +0000 (17:25 +0200)]
Remove old "statistics" module with R factors etc

compare_hkl does all of these, much better than these functions.

2 months agoRemove "valid" item from "struct imagefeature"
Thomas White [Tue, 7 May 2019 15:21:05 +0000 (17:21 +0200)]
Remove "valid" item from "struct imagefeature"

2 months agogpu_sim_check: Increase tolerance from 1% to 1.1%
Thomas White [Tue, 14 May 2019 08:02:02 +0000 (10:02 +0200)]
gpu_sim_check: Increase tolerance from 1% to 1.1%

1.03% deviation was observed in the wild, with no apparent problems.

2 months agoFussiness
Thomas White [Mon, 13 May 2019 13:44:23 +0000 (15:44 +0200)]
Fussiness

2 months agogpu_sim_check: Succeed if GPU not available
Thomas White [Mon, 13 May 2019 13:41:54 +0000 (15:41 +0200)]
gpu_sim_check: Succeed if GPU not available

On recent OSes, OpenCL (the API) is always available, but a GPU device
not always.  Therefore, this test will always be built, and shouldn't
fail just because a GPU isn't present.

2 months agocheck_hkl: Report overall completeness and redundancy
Thomas White [Wed, 8 May 2019 11:26:27 +0000 (13:26 +0200)]
check_hkl: Report overall completeness and redundancy

2 months agocheck_hkl: Use unsigned long for reflection counts
Thomas White [Wed, 8 May 2019 11:26:11 +0000 (13:26 +0200)]
check_hkl: Use unsigned long for reflection counts

2 months agoAdd missing =n
Thomas White [Wed, 8 May 2019 08:41:36 +0000 (10:41 +0200)]
Add missing =n

2 months agoFormatting
Thomas White [Wed, 8 May 2019 08:32:36 +0000 (10:32 +0200)]
Formatting

2 months agoRemove unused code
Yaroslav Gevorkov [Tue, 7 May 2019 17:27:26 +0000 (19:27 +0200)]
Remove unused code

2 months agoAdd new xgandalf options
Yaroslav Gevorkov [Tue, 7 May 2019 17:26:57 +0000 (19:26 +0200)]
Add new xgandalf options

2 months agoDon't try to build API docs unless DOXYGEN_FOUND
Thomas White [Tue, 7 May 2019 14:36:39 +0000 (16:36 +0200)]
Don't try to build API docs unless DOXYGEN_FOUND

2 months agoMerge branch 'tom/doxygen'
Thomas White [Tue, 7 May 2019 14:27:18 +0000 (16:27 +0200)]
Merge branch 'tom/doxygen'

2 months agoRemove intmat_set_all_3x3()
Thomas White [Tue, 7 May 2019 12:06:36 +0000 (14:06 +0200)]
Remove intmat_set_all_3x3()

2 months agoAdd CrystFEL version (including API revision) directly into Doxygen main page
Thomas White [Tue, 7 May 2019 14:21:42 +0000 (16:21 +0200)]
Add CrystFEL version (including API revision) directly into Doxygen main page

2 months agoUpdate all source code comments to Doxygen format
Thomas White [Tue, 7 May 2019 14:10:17 +0000 (16:10 +0200)]
Update all source code comments to Doxygen format

2 months agoMain and coding standard pages
Thomas White [Tue, 7 May 2019 14:09:35 +0000 (16:09 +0200)]
Main and coding standard pages

2 months agoAdd CMake stuff for Doxygen
Thomas White [Tue, 7 May 2019 14:08:59 +0000 (16:08 +0200)]
Add CMake stuff for Doxygen

2 months agoRemove old documentation stuff
Thomas White [Thu, 2 May 2019 14:26:06 +0000 (16:26 +0200)]
Remove old documentation stuff

2 months agoMove spectrum type enum to pattern_sim.c
Thomas White [Fri, 3 May 2019 08:24:12 +0000 (10:24 +0200)]
Move spectrum type enum to pattern_sim.c

3 months agoClean up residual CBFlib stuff
Thomas White [Tue, 16 Apr 2019 15:25:50 +0000 (17:25 +0200)]
Clean up residual CBFlib stuff

3 months agoRecognise (if not handle) all CBF formats
Thomas White [Tue, 16 Apr 2019 13:56:50 +0000 (15:56 +0200)]
Recognise (if not handle) all CBF formats

3 months agoBasic CBF reader with byte offset decompression
Thomas White [Mon, 15 Apr 2019 16:28:54 +0000 (18:28 +0200)]
Basic CBF reader with byte offset decompression

3 months agoStrip ouf CBFlib references
Thomas White [Fri, 22 Mar 2019 12:56:49 +0000 (13:56 +0100)]
Strip ouf CBFlib references

3 months agomove-entire-detector: Add z direction
Thomas White [Fri, 12 Apr 2019 13:20:26 +0000 (15:20 +0200)]
move-entire-detector: Add z direction

3 months agocell_explorer: Exclude cells when centering type is set to grey
Thomas White [Wed, 10 Apr 2019 14:13:51 +0000 (16:13 +0200)]
cell_explorer: Exclude cells when centering type is set to grey

This is more useful than just changing the colours.  Fixes CRYS-224.